In this paper, a system identification for control procedure of a main irrigation canal pool characterized by exhibiting large variations in their dynamical parameters when it discharge regimes change is developed. This procedure delivers not only a nominal model, but also a reliable estimate of the canal pool parametric uncertainty associated with the model. The complete identification for control procedure from experiment design to model validation taking into account prior physical information is presented. It is shown that a linear second order model with an ARMAX structure and a time delay describes adequately the main nominal dynamical behavior of this canal pool. Application of system identification for control in control system design of water distribution in main irrigation canal pools responds to the current necessity of introducing more effective and robust control systems. Copyright © 2007 International Federation of Automatic Control All Rights Reserved.